Will I need two Firewire inputs in my computer or can I use one of the Firewire inputs in a unit as a "thru" for the other? In that case will the FW 400 suffice? I know there are bandwidth issues…
You can daisy-chain the FireWire connections as long as you don't use the FW as a power supply for "downstream" equipment – your computer only need one FW connector.
Not sure what the bandwidth limit is – FW400 is bus limited at 49mB/s (about 250 48kHz channels), but the computer hardware/software will most likely be the limiting factor. Again, the best computer you can find would be good.